3dECM crash

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1

Hello AFNI friends,

I was trying to experiment with some of the network(ish) tools in AFNI. I ran 3dECM with the following syntax:


3dECM -fecm -mask /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz -prefix 150926_20176_3dECM.nii.gz filt_denoised_func_data_nonaggr_MNI_wmcsf.nii.gz

[Which is a resting state scan, denoised with ICA-AROMA with wm, csf, and motion nuisance regressors (also bandpassing)…

And I got the following out:


++ 3dECM: AFNI version=AFNI_17.3.09 (Dec 22 2017) [64-bit]
++ 228453 voxels in -mask dataset
++ vectim-izing input dataset
++ Detrending with polort = 1
++ Calculating ECM with FECM (sparsity=100.000%,thresh=-1.200,
  scale=0.500, shift=1.000, max_iter=10000, eps=0.000, binary=0)
creating output bucket(150926_20176_3dECM.nii.gz)
 + creating output dataset in memory
*** Error in `3dECM': munmap_chunk(): invalid pointer: 0x00000000004072eb ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fa0239437e5]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7fa023950698]
3dECM[0x44fb76]
3dECM[0x40b760]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fa0238ec830]
3dECM[0x408169]
======= Memory map: ========
00400000-008f0000 r-xp 00000000 09:01 4203479                            /usr/local/pkg/afni/3dECM
00aef000-00b39000 rw-p 004ef000 09:01 4203479                            /usr/local/pkg/afni/3dECM
00b39000-00b94000 rw-p 00000000 00:00 0
01d5b000-31ccd000 rw-p 00000000 00:00 0                                  [heap]
7fa0218d7000-7fa0218ed000 r-xp 00000000 09:01 9437272                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7fa0218ed000-7fa021aec000 ---p 00016000 09:01 9437272                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7fa021aec000-7fa021aed000 r--p 00015000 09:01 9437272                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7fa021aed000-7fa021aee000 rw-p 00016000 09:01 9437272                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7fa021aee000-7fa021af9000 r-xp 00000000 09:01 9444387                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7fa021af9000-7fa021cf8000 ---p 0000b000 09:01 9444387                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7fa021cf8000-7fa021cf9000 r--p 0000a000 09:01 9444387                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7fa021cf9000-7fa021cfa000 rw-p 0000b000 09:01 9444387                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7fa021cfa000-7fa021d00000 rw-p 00000000 00:00 0
7fa021d00000-7fa021d0b000 r-xp 00000000 09:01 9444400                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7fa021d0b000-7fa021f0a000 ---p 0000b000 09:01 9444400                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7fa021f0a000-7fa021f0b000 r--p 0000a000 09:01 9444400                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7fa021f0b000-7fa021f0c000 rw-p 0000b000 09:01 9444400                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7fa021f0c000-7fa021f22000 r-xp 00000000 09:01 9441203                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7fa021f22000-7fa022121000 ---p 00016000 09:01 9441203                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7fa022121000-7fa022122000 r--p 00015000 09:01 9441203                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7fa022122000-7fa022123000 rw-p 00016000 09:01 9441203                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7fa022123000-7fa022125000 rw-p 00000000 00:00 0
7fa022125000-7fa02212d000 r-xp 00000000 09:01 9444406                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7fa02212d000-7fa02232c000 ---p 00008000 09:01 9444406                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7fa02232c000-7fa02232d000 r--p 00007000 09:01 9444406                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7fa02232d000-7fa02232e000 rw-p 00008000 09:01 9444406                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7fa02232e000-7fa022333000 r-xp 00000000 09:01 1054227                    /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7fa022333000-7fa022532000 ---p 00005000 09:01 1054227                    /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7fa022532000-7fa022533000 r--p 00004000 09:01 1054227                    /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7fa022533000-7fa022534000 rw-p 00005000 09:01 1054227                    /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7fa022534000-7fa02255a000 r-xp 00000000 09:01 9437368                    /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7fa02255a000-7fa02275a000 ---p 00026000 09:01 9437368                    /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7fa02275a000-7fa02275c000 r--p 00026000 09:01 9437368                    /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7fa02275c000-7fa02275d000 rw-p 00028000 09:01 9437368                    /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7fa02275d000-7fa02277e000 r-xp 00000000 09:01 1054229                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fa02277e000-7fa02297d000 ---p 00021000 09:01 1054229                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fa02297d000-7fa02297e000 r--p 00020000 09:01 1054229                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fa02297e000-7fa02297f000 rw-p 00021000 09:01 1054229                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fa02297f000-7fa022983000 r-xp 00000000 09:01 9437217                    /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7fa022983000-7fa022b82000 ---p 00004000 09:01 9437217                    /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7fa022b82000-7fa022b83000 r--p 00003000 09:01 9437217                    /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7fa022b83000-7fa022b84000 rw-p 00004000 09:01 9437217                    /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7fa022b84000-7fa022b86000 r-xp 00000000 09:01 1054225                    /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7fa022b86000-7fa022d86000 ---p 00002000 09:01 1054225                    /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7fa022d86000-7fa022d87000 r--p 00002000 09:01 1054225                    /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7fa022d87000-7fa022d88000 rw-p 00003000 09:01 1054225                    /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7fa022d88000-7fa022d91000 r-xp 00000000 09:01 1057985                    /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7fa022d91000-7fa022f90000 ---p 00009000 09:01 1057985                    /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7fa022f90000-7fa022f91000 r--p 00008000 09:01 1057985                    /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7fa022f91000-7fa022f92000 rw-p 00009000 09:01 1057985                    /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7fa022f92000-7fa023036000 r-xp 00000000 09:01 1048654                    /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7fa023036000-7fa023235000 ---p 000a4000 09:01 1048654                    /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7fa023235000-7fa02323b000 r--p 000a3000 09:01 1048654                    /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7fa02323b000-7fa02323c000 rw-p 000a9000 09:01 1048654                    /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7fa02323c000-7fa023279000 r-xp 00000000 09:01 1057901                    /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7fa023279000-7fa023478000 ---p 0003d000 09:01 1057901                    /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7fa023478000-7fa02347a000 r--p 0003c000 09:01 1057901                    /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7fa02347a000-7fa02347f000 rw-p 0003e000 09:01 1057901                    /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7fa02347f000-7fa023497000 r-xp 00000000 09:01 9444398                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fa023497000-7fa023696000 ---p 00018000 09:01 9444398                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fa023696000-7fa023697000 r--p 00017000 09:01 9444398                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fa023697000-7fa023698000 rw-p 00018000 09:01 9444398                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fa023698000-7fa02369c000 rw-p 00000000 00:00 0
7fa02369c000-7fa0236ca000 r-xp 00000000 09:01 1050685                    /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa0236ca000-7fa0238ca000 ---p 0002e000 09:01 1050685                    /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa0238ca000-7fa0238cb000 r--p 0002e000 09:01 1050685                    /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa0238cb000-7fa0238cc000 rw-p 0002f000 09:01 1050685                    /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa0238cc000-7fa023a8c000 r-xp 00000000 09:01 9444416                    /lib/x86_64-linux-gnu/libc-2.23.so
7fa023a8c000-7fa023c8c000 ---p 001c0000 09:01 9444416                    /lib/x86_64-linux-gnu/libc-2.23.so
7fa023c8c000-7fa023c90000 r--p 001c0000 09:01 9444416                    /lib/x86_64-linux-gnu/libc-2.23.so
7fa023c90000-7fa023c92000 rw-p 001c4000 09:01 9444416                    /lib/x86_64-linux-gnu/libc-2.23.so
7fa023c92000-7fa023c96000 rw-p 00000000 00:00 0
7fa023c96000-7fa023c99000 r-xp 00000000 09:01 9444405                    /lib/x86_64-linux-gnu/libdl-2.23.so
7fa023c99000-7fa023e98000 ---p 00003000 09:01 9444405                    /lib/x86_64-linux-gnu/libdl-2.23.so
7fa023e98000-7fa023e99000 r--p 00002000 09:01 9444405                    /lib/x86_64-linux-gnu/libdl-2.23.so
7fa023e99000-7fa023e9a000 rw-p 00003000 09:01 9444405                    /lib/x86_64-linux-gnu/libdl-2.23.so
7fa023e9a000-7fa023fa2000 r-xp 00000000 09:01 9444411                    /lib/x86_64-linux-gnu/libm-2.23.so
7fa023fa2000-7fa0241a1000 ---p 00108000 09:01 9444411                    /lib/x86_64-linux-gnu/libm-2.23.so
7fa0241a1000-7fa0241a2000 r--p 00107000 09:01 9444411                    /lib/x86_64-linux-gnu/libm-2.23.so
7fa0241a2000-7fa0241a3000 rw-p 00108000 09:01 9444411                    /lib/x86_64-linux-gnu/libm-2.23.so
7fa0241a3000-7fa0241bc000 r-xp 00000000 09:01 9447283                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7fa0241bc000-7fa0243bb000 ---p 00019000 09:01 9447283                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7fa0243bb000-7fa0243bc000 r--p 00018000 09:01 9447283                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7fa0243bc000-7fa0243bd000 rw-p 00019000 09:01 9447283                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7fa0243bd000-7fa0243e1000 r-xp 00000000 09:01 9437770                    /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7fa0243e1000-7fa0245e0000 ---p 00024000 09:01 9437770                    /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7fa0245e0000-7fa0245e1000 r--p 00023000 09:01 9437770                    /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7fa0245e1000-7fa0245e2000 rw-p 00024000 09:01 9437770                    /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7fa0245e2000-7fa024717000 r-xp 00000000 09:01 1054244                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fa024717000-7fa024917000 ---p 00135000 09:01 1054244                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fa024917000-7fa024918000 r--p 00135000 09:01 1054244                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fa024918000-7fa02491c000 rw-p 00136000 09:01 1054244                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fa02491c000-7fa024932000 r-xp 00000000 09:01 1057914                    /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7fa024932000-7fa024b31000 ---p 00016000 09:01 1057914                    /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7fa024b31000-7fa024b32000 r--p 00015000 09:01 1057914                    /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7fa024b32000-7fa024b33000 rw-p 00016000 09:01 1057914                    /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7fa024b33000-7fa024b36000 rw-p 00000000 00:00 0
7fa024b36000-7fa024b3d000 r-xp 00000000 09:01 1057916                    /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7fa024b3d000-7fa024d3c000 ---p 00007000 09:01 1057916                    /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7fa024d3c000-7fa024d3d000 r--p 00006000 09:01 1057916                    /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7fa024d3d000-7fa024d3e000 rw-p 00007000 09:01 1057916                    /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7fa024d3e000-7fa024d56000 r-xp 00000000 09:01 1058207                    /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7fa024d56000-7fa024f55000 ---p 00018000 09:01 1058207                    /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7fa024f55000-7fa024f56000 r--p 00017000 09:01 1058207                    /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7fa024f56000-7fa024f57000 rw-p 00018000 09:01 1058207                    /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7fa024f57000-7fa024f68000 r-xp 00000000 09:01 1054246                    /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7fa024f68000-7fa025167000 ---p 00011000 09:01 1054246                    /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7fa025167000-7fa025168000 r--p 00010000 09:01 1054246                    /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7fa025168000-7fa025169000 rw-p 00011000 09:01 1054246                    /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7fa025169000-7fa025179000 r-xp 00000000 09:01 1048937                    /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7fa025179000-7fa025379000 ---p 00010000 09:01 1048937                    /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7fa025379000-7fa02537a000 r--p 00010000 09:01 1048937                    /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7fa02537a000-7fa02537b000 rw-p 00011000 09:01 1048937                    /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7fa02537b000-7fa025383000 r-xp 00000000 09:01 1062363                    /usr/local/lib/libXp.so.6.2.0
7fa025383000-7fa025582000 ---p 00008000 09:01 1062363                    /usr/local/lib/libXp.so.6.2.0
7fa025582000-7fa025583000 r--p 00007000 09:01 1062363                    /usr/local/lib/libXp.so.6.2.0
7fa025583000-7fa025584000 rw-p 00008000 09:01 1062363                    /usr/local/lib/libXp.so.6.2.0
7fa025584000-7fa025598000 r-xp 00000000 09:01 1057991                    /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7fa025598000-7fa025797000 ---p 00014000 09:01 1057991                    /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7fa025797000-7fa025798000 r--p 00013000 09:01 1057991                    /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7fa025798000-7fa025799000 rw-p 00014000 09:01 1057991                    /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7fa025799000-7fa0257fb000 r-xp 00000000 09:01 1057918                    /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7fa0257fb000-7fa0259fb000 ---p 00062000 09:01 1057918                    /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7fa0259fb000-7fa0259fc000 r--p 00062000 09:01 1057918                    /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7fa0259fc000-7fa025a01000 rw-p 00063000 09:01 1057918                    /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7fa025a01000-7fa025a02000 rw-p 00000000 00:00 0
7fa025a02000-7fa025a28000 r-xp 00000000 09:01 9441205                    /lib/x86_64-linux-gnu/ld-2.23.so
7fa025bf3000-7fa025bff000 rw-p 00000000 00:00 0
7fa025c24000-7fa025c27000 rw-p 00000000 00:00 0
7fa025c27000-7fa025c28000 r--p 00025000 09:01 9441205                    /lib/x86_64-linux-gnu/ld-2.23.so
7fa025c28000-7fa025c29000 rw-p 00026000 09:01 9441205                    /lib/x86_64-linux-gnu/ld-2.23.so
7fa025c29000-7fa025c2a000 rw-p 00000000 00:00 0
7ffc4ad1c000-7ffc4ad3d000 rw-p 00000000 00:00 0                          [stack]
7ffc4adee000-7ffc4adf0000 r--p 00000000 00:00 0                          [vvar]
7ffc4adf0000-7ffc4adf2000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

Fatal Signal 6 (SIGABRT) received
  3dECM main
 Bottom of Debug Stack
** Command line was:
3dECM -fecm -mask /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz -prefix 150926_20176_3dECM.nii.gz filt_denoised_func_data_nonaggr_MNI_wmcsf.nii.gz
** AFNI version = AFNI_17.3.09  Compile date = Dec 22 2017
** [[Precompiled binary linux_openmp_64: Dec 22 2017]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/jamielh/.afni.crashlog

I’m no expert, but that didn’t look good. Anyone else run into similar issues? Did I somehow break my server’s memory? [My IT folks are really going to be pissed at me if so… 8-))

Thanks in advance for any thoughts!
Jamie.

2

I tried to increase the memory used by the program, but no dice… I ran:


3dECM -fecm -memory 20 -mask /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz filt_denoised_func_data_nonaggr_MNI_wmcsf.nii.gz

but got out…


++ 3dECM: AFNI version=AFNI_17.3.09 (Dec 22 2017) [64-bit]
++ 228453 voxels in -mask dataset
++ vectim-izing input dataset
++ Detrending with polort = 1
++ Calculating ECM with FECM (sparsity=100.000%,thresh=-1.200,
  scale=0.500, shift=1.000, max_iter=10000, eps=0.000, binary=0)
creating output bucket(ECM)
 + creating output dataset in memory
*** Error in `3dECM': munmap_chunk(): invalid pointer: 0x00000000004072eb ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f269a2e67e5]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7f269a2f3698]
3dECM[0x44fb76]
3dECM[0x40b760]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f269a28f830]
3dECM[0x408169]
======= Memory map: ========
00400000-008f0000 r-xp 00000000 09:01 21381388                           /usr/local/pkg/afni/3dECM
00aef000-00b39000 rw-p 004ef000 09:01 21381388                           /usr/local/pkg/afni/3dECM
00b39000-00b94000 rw-p 00000000 00:00 0
024d9000-3244b000 rw-p 00000000 00:00 0                                  [heap]
7f2698289000-7f269829f000 r-xp 00000000 09:01 1311241                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f269829f000-7f269849e000 ---p 00016000 09:01 1311241                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f269849e000-7f269849f000 rw-p 00015000 09:01 1311241                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f269849f000-7f26984aa000 r-xp 00000000 09:01 1315230                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f26984aa000-7f26986a9000 ---p 0000b000 09:01 1315230                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f26986a9000-7f26986aa000 r--p 0000a000 09:01 1315230                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f26986aa000-7f26986ab000 rw-p 0000b000 09:01 1315230                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f26986ab000-7f26986b1000 rw-p 00000000 00:00 0
7f26986b1000-7f26986bc000 r-xp 00000000 09:01 1315233                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f26986bc000-7f26988bb000 ---p 0000b000 09:01 1315233                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f26988bb000-7f26988bc000 r--p 0000a000 09:01 1315233                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f26988bc000-7f26988bd000 rw-p 0000b000 09:01 1315233                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f26988bd000-7f26988d3000 r-xp 00000000 09:01 1311133                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7f26988d3000-7f2698ad2000 ---p 00016000 09:01 1311133                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7f2698ad2000-7f2698ad3000 r--p 00015000 09:01 1311133                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7f2698ad3000-7f2698ad4000 rw-p 00016000 09:01 1311133                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7f2698ad4000-7f2698ad6000 rw-p 00000000 00:00 0
7f2698ad6000-7f2698ade000 r-xp 00000000 09:01 1315239                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f2698ade000-7f2698cdd000 ---p 00008000 09:01 1315239                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f2698cdd000-7f2698cde000 r--p 00007000 09:01 1315239                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f2698cde000-7f2698cdf000 rw-p 00008000 09:01 1315239                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f2698cdf000-7f2698ce4000 r-xp 00000000 09:01 18356442                   /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f2698ce4000-7f2698ee3000 ---p 00005000 09:01 18356442                   /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f2698ee3000-7f2698ee4000 r--p 00004000 09:01 18356442                   /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f2698ee4000-7f2698ee5000 rw-p 00005000 09:01 18356442                   /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f2698ee5000-7f2698f0b000 r-xp 00000000 09:01 1310868                    /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f2698f0b000-7f269910b000 ---p 00026000 09:01 1310868                    /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f269910b000-7f269910d000 r--p 00026000 09:01 1310868                    /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f269910d000-7f269910e000 rw-p 00028000 09:01 1310868                    /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f269910e000-7f269912f000 r-xp 00000000 09:01 18356444                   /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f269912f000-7f269932e000 ---p 00021000 09:01 18356444                   /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f269932e000-7f269932f000 r--p 00020000 09:01 18356444                   /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f269932f000-7f2699330000 rw-p 00021000 09:01 18356444                   /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f2699330000-7f2699334000 r-xp 00000000 09:01 1310814                    /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f2699334000-7f2699533000 ---p 00004000 09:01 1310814                    /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f2699533000-7f2699534000 r--p 00003000 09:01 1310814                    /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f2699534000-7f2699535000 rw-p 00004000 09:01 1310814                    /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f2699535000-7f2699537000 r-xp 00000000 09:01 18356440                   /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f2699537000-7f2699737000 ---p 00002000 09:01 18356440                   /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f2699737000-7f2699738000 r--p 00002000 09:01 18356440                   /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f2699738000-7f2699739000 rw-p 00003000 09:01 18356440                   /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f2699739000-7f2699742000 r-xp 00000000 09:01 18356672                   /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f2699742000-7f2699941000 ---p 00009000 09:01 18356672                   /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f2699941000-7f2699942000 r--p 00008000 09:01 18356672                   /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f2699942000-7f2699943000 rw-p 00009000 09:01 18356672                   /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f2699943000-7f26999e7000 r-xp 00000000 09:01 18355823                   /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7f26999e7000-7f2699be6000 ---p 000a4000 09:01 18355823                   /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7f2699be6000-7f2699bec000 r--p 000a3000 09:01 18355823                   /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7f2699bec000-7f2699bed000 rw-p 000a9000 09:01 18355823                   /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7f2699bed000-7f2699c2a000 r-xp 00000000 09:01 18356501                   /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7f2699c2a000-7f2699e29000 ---p 0003d000 09:01 18356501                   /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7f2699e29000-7f2699e2b000 r--p 0003c000 09:01 18356501                   /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7f2699e2b000-7f2699e30000 rw-p 0003e000 09:01 18356501                   /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7f2699e30000-7f2699e48000 r-xp 00000000 09:01 1315232                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7f2699e48000-7f269a047000 ---p 00018000 09:01 1315232                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7f269a047000-7f269a048000 r--p 00017000 09:01 1315232                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7f269a048000-7f269a049000 rw-p 00018000 09:01 1315232                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7f269a049000-7f269a04d000 rw-p 00000000 00:00 0
7f269a04d000-7f269a06e000 r-xp 00000000 09:01 18350631                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f269a06e000-7f269a26d000 ---p 00021000 09:01 18350631                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f269a26d000-7f269a26e000 r--p 00020000 09:01 18350631                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f269a26e000-7f269a26f000 rw-p 00021000 09:01 18350631                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f269a26f000-7f269a42f000 r-xp 00000000 09:01 1315249                    /lib/x86_64-linux-gnu/libc-2.23.so
7f269a42f000-7f269a62f000 ---p 001c0000 09:01 1315249                    /lib/x86_64-linux-gnu/libc-2.23.so
7f269a62f000-7f269a633000 r--p 001c0000 09:01 1315249                    /lib/x86_64-linux-gnu/libc-2.23.so
7f269a633000-7f269a635000 rw-p 001c4000 09:01 1315249                    /lib/x86_64-linux-gnu/libc-2.23.so
7f269a635000-7f269a639000 rw-p 00000000 00:00 0
7f269a639000-7f269a63c000 r-xp 00000000 09:01 1315238                    /lib/x86_64-linux-gnu/libdl-2.23.so
7f269a63c000-7f269a83b000 ---p 00003000 09:01 1315238                    /lib/x86_64-linux-gnu/libdl-2.23.so
7f269a83b000-7f269a83c000 r--p 00002000 09:01 1315238                    /lib/x86_64-linux-gnu/libdl-2.23.so
7f269a83c000-7f269a83d000 rw-p 00003000 09:01 1315238                    /lib/x86_64-linux-gnu/libdl-2.23.so
7f269a83d000-7f269a945000 r-xp 00000000 09:01 1315244                    /lib/x86_64-linux-gnu/libm-2.23.so
7f269a945000-7f269ab44000 ---p 00108000 09:01 1315244                    /lib/x86_64-linux-gnu/libm-2.23.so
7f269ab44000-7f269ab45000 r--p 00107000 09:01 1315244                    /lib/x86_64-linux-gnu/libm-2.23.so
7f269ab45000-7f269ab46000 rw-p 00108000 09:01 1315244                    /lib/x86_64-linux-gnu/libm-2.23.so
7f269ab46000-7f269ab5f000 r-xp 00000000 09:01 1311192                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7f269ab5f000-7f269ad5e000 ---p 00019000 09:01 1311192                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7f269ad5e000-7f269ad5f000 r--p 00018000 09:01 1311192                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7f269ad5f000-7f269ad60000 rw-p 00019000 09:01 1311192                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7f269ad60000-7f269ad84000 r-xp 00000000 09:01 1311297                    /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7f269ad84000-7f269af83000 ---p 00024000 09:01 1311297                    /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7f269af83000-7f269af84000 r--p 00023000 09:01 1311297                    /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7f269af84000-7f269af85000 rw-p 00024000 09:01 1311297                    /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7f269af85000-7f269b0ba000 r-xp 00000000 09:01 18356447                   /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f269b0ba000-7f269b2ba000 ---p 00135000 09:01 18356447                   /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f269b2ba000-7f269b2bb000 r--p 00135000 09:01 18356447                   /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f269b2bb000-7f269b2bf000 rw-p 00136000 09:01 18356447                   /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f269b2bf000-7f269b2d5000 r-xp 00000000 09:01 18357425                   /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f269b2d5000-7f269b4d4000 ---p 00016000 09:01 18357425                   /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f269b4d4000-7f269b4d5000 r--p 00015000 09:01 18357425                   /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f269b4d5000-7f269b4d6000 rw-p 00016000 09:01 18357425                   /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f269b4d6000-7f269b4d9000 rw-p 00000000 00:00 0
7f269b4d9000-7f269b4e0000 r-xp 00000000 09:01 18357427                   /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f269b4e0000-7f269b6df000 ---p 00007000 09:01 18357427                   /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f269b6df000-7f269b6e0000 r--p 00006000 09:01 18357427                   /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f269b6e0000-7f269b6e1000 rw-p 00007000 09:01 18357427                   /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f269b6e1000-7f269b6f9000 r-xp 00000000 09:01 18358348                   /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7f269b6f9000-7f269b8f8000 ---p 00018000 09:01 18358348                   /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7f269b8f8000-7f269b8f9000 r--p 00017000 09:01 18358348                   /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7f269b8f9000-7f269b8fa000 rw-p 00018000 09:01 18358348                   /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7f269b8fa000-7f269b90b000 r-xp 00000000 09:01 18356449                   /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f269b90b000-7f269bb0a000 ---p 00011000 09:01 18356449                   /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f269bb0a000-7f269bb0b000 r--p 00010000 09:01 18356449                   /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f269bb0b000-7f269bb0c000 rw-p 00011000 09:01 18356449                   /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f269bb0c000-7f269bb1c000 r-xp 00000000 09:01 18358350                   /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7f269bb1c000-7f269bd1c000 ---p 00010000 09:01 18358350                   /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7f269bd1c000-7f269bd1d000 r--p 00010000 09:01 18358350                   /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7f269bd1d000-7f269bd1e000 rw-p 00011000 09:01 18358350                   /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7f269bd1e000-7f269bd26000 r-xp 00000000 09:01 18362216                   /usr/lib/x86_64-linux-gnu/libXp.so.6.2.0
7f269bd26000-7f269bf25000 ---p 00008000 09:01 18362216                   /usr/lib/x86_64-linux-gnu/libXp.so.6.2.0
7f269bf25000-7f269bf26000 r--p 00007000 09:01 18362216                   /usr/lib/x86_64-linux-gnu/libXp.so.6.2.0
7f269bf26000-7f269bf27000 rw-p 00008000 09:01 18362216                   /usr/lib/x86_64-linux-gnu/libXp.so.6.2.0
7f269bf27000-7f269bf3b000 r-xp 00000000 09:01 18357701                   /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7f269bf3b000-7f269c13a000 ---p 00014000 09:01 18357701                   /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7f269c13a000-7f269c13b000 r--p 00013000 09:01 18357701                   /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7f269c13b000-7f269c13c000 rw-p 00014000 09:01 18357701                   /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7f269c13c000-7f269c19e000 r-xp 00000000 09:01 18357429                   /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f269c19e000-7f269c39e000 ---p 00062000 09:01 18357429                   /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f269c39e000-7f269c39f000 r--p 00062000 09:01 18357429                   /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f269c39f000-7f269c3a4000 rw-p 00063000 09:01 18357429                   /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f269c3a4000-7f269c3a5000 rw-p 00000000 00:00 0
7f269c3a5000-7f269c3cb000 r-xp 00000000 09:01 1315227                    /lib/x86_64-linux-gnu/ld-2.23.so
7f269c59a000-7f269c5a6000 rw-p 00000000 00:00 0
7f269c5c7000-7f269c5ca000 rw-p 00000000 00:00 0
7f269c5ca000-7f269c5cb000 r--p 00025000 09:01 1315227                    /lib/x86_64-linux-gnu/ld-2.23.so
7f269c5cb000-7f269c5cc000 rw-p 00026000 09:01 1315227                    /lib/x86_64-linux-gnu/ld-2.23.so
7f269c5cc000-7f269c5cd000 rw-p 00000000 00:00 0
7ffc202c2000-7ffc202e3000 rw-p 00000000 00:00 0                          [stack]
7ffc203f3000-7ffc203f5000 r--p 00000000 00:00 0                          [vvar]
7ffc203f5000-7ffc203f7000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

Fatal Signal 6 (SIGABRT) received
  3dECM main
 Bottom of Debug Stack
** Command line was:
3dECM -fecm -memory 20 -mask /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz filt_denoised_func_data_nonaggr_MNI_wmcsf.nii.gz
** AFNI version = AFNI_17.3.09  Compile date = Dec 22 2017
** [[Precompiled binary linux_openmp_64: Dec 22 2017]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/jamielh/.afni.crashlog

Folks have any thoughts on this one?

3

Hello Jamie,

I will look into the issue and let you know if I need any more information. It might be a few days before I can get it fixed.

The memory might have been banged up a bit, but should recover quickly. No reason for the sys admins to be too upset with you.

Cheers,
Cameronj

4

Hey,

It looks like 3dECM still does not work. However, is there any way to just get the correlation matrix (for all pairs of voxels) in a given masked region, without the following eigenvector calculation? Or is there any other command in AFNI could do this? Thanks!

Qiuhai

5

Maybe 3dTcorrMap with the -mask and the -CorrMask options is what you want.